One anecdote: Mr. Goenka ends every day with 'May all beings be happy.' Imagine my surprise when the server said we could not pet the stray cats that were walking around, to prevent them from coming back all the time, because they didn't want to take care of them.
Some of these contradictions started to annoy me, and almost made me leave, until I realized on day 5 that this is all part of the meditation, more or less. I wasn't there for them, I was there for my own development, and so I had to accept the reality as it is, stop comparing and focus on the experience. All externalities are not relevant, and the ability to not let your mood be influenced by things outside your control is exactly what is developed there. So every contradiction or irritation became a challenge, to strengthen my discipline.
I had an interesting conversation on the last day with a Buddhist. He also didn't like the 'one true way' part of it. He became a Buddhist mainly because his teacher told him honestly that his way was just one of many that one can follow.
And although Mr Goenka says it's the one true way, he also continuously says that you should not take his (or anyone else's) words for granted, but that you should experience and decide for yourself, and that whatever you do, decide on a path to follow and stay with it, because if you start a new path all the time, you will never reach the end of the road.